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fix_npt_sphere.cpp
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Sat, Jun 28, 16:48

fix_npt_sphere.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "fix_npt_sphere.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "compute.h"
#include "kspace.h"
#include "update.h"
#include "domain.h"
#include "error.h"
using namespace LAMMPS_NS;
#define INERTIA 0.4 // moment of inertia for sphere
enum{NOBIAS,BIAS};
/* ---------------------------------------------------------------------- */
FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) :
FixNPT(lmp, narg, arg)
{
if (!atom->omega_flag || !atom->torque_flag)
error->all("Fix nvt/sphere requires atom attributes omega, torque");
dttype = new double[atom->ntypes+1];
}
/* ---------------------------------------------------------------------- */
FixNPTSphere::~FixNPTSphere()
{
delete [] dttype;
}
/* ---------------------------------------------------------------------- */
void FixNPTSphere::init()
{
FixNPT::init();
if (!atom->shape)
error->all("Fix npt/sphere requires atom attribute shape");
double **shape = atom->shape;
for (int i = 1; i <= atom->ntypes; i++)
if (shape[i][0] != shape[i][1] || shape[i][0] != shape[i][2])
error->all("Fix npt/sphere requires spherical particle shapes");
}
/* ----------------------------------------------------------------------
1st half of Verlet update
------------------------------------------------------------------------- */
void FixNPTSphere::initial_integrate(int vflag)
{
int i;
double dtfm,dtirotate;
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
// update eta_dot
t_target = t_start + delta * (t_stop-t_start);
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
eta_dot += f_eta*dthalf;
eta_dot *= drag_factor;
eta += dtv*eta_dot;
// update omega_dot
// for non-varying dims, p_freq is 0.0, so omega_dot doesn't change
double f_omega,volume;
if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd;
else volume = domain->xprd*domain->yprd;
double denskt = atom->natoms*boltz*t_target / volume * nktv2p;
for (i = 0; i < 3; i++) {
p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
f_omega = p_freq[i]*p_freq[i] * (p_current[i]-p_target[i])/denskt;
omega_dot[i] += f_omega*dthalf;
omega_dot[i] *= drag_factor;
omega[i] += dtv*omega_dot[i];
factor[i] = exp(-dthalf*(eta_dot+omega_dot[i]));
dilation[i] = exp(dthalf*omega_dot[i]);
}
factor_rotate = exp(-dthalf*eta_dot);
// v update only for atoms in group
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (which == NOBIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
}
}
} else if (which == BIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
temperature->restore_bias(i,v[i]);
}
}
}
// remap simulation box and all owned atoms by 1/2 step
remap(0);
// x update by full step only for atoms in group
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
// recompute timesteps since dt may have changed or come via rRESPA
double dtfrotate = dtf / INERTIA;
int ntypes = atom->ntypes;
double **shape = atom->shape;
for (int i = 1; i <= ntypes; i++)
dttype[i] = dtfrotate / (shape[i][0]*shape[i][0]*mass[i]);
// update angular momentum by 1/2 step
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtirotate = dttype[type[i]];
omega[i][0] = omega[i][0]*factor_rotate + dtirotate*torque[i][0];
omega[i][1] = omega[i][1]*factor_rotate + dtirotate*torque[i][1];
omega[i][2] = omega[i][2]*factor_rotate + dtirotate*torque[i][2];
}
}
// remap simulation box and all owned atoms by 1/2 step
// redo KSpace coeffs since volume has changed
remap(0);
if (kspace_flag) force->kspace->setup();
}
/* ----------------------------------------------------------------------
2nd half of Verlet update
------------------------------------------------------------------------- */
void FixNPTSphere::final_integrate()
{
int i,itype;
double dtfm,dtirotate;
// v update only for atoms in group
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// recompute timesteps since dt may have changed or come via rRESPA
double dtfrotate = dtf / INERTIA;
int ntypes = atom->ntypes;
double **shape = atom->shape;
for (int i = 1; i <= ntypes; i++)
dttype[i] = dtfrotate / (shape[i][0]*shape[i][0]*mass[i]);
if (which == NOBIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtfm = dtf / mass[itype];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
dtirotate = dttype[itype];
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) * factor_rotate;
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) * factor_rotate;
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) * factor_rotate;
}
}
} else if (which == BIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
temperature->remove_bias(i,v[i]);
dtfm = dtf / mass[itype];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
temperature->restore_bias(i,v[i]);
dtirotate = dttype[itype];
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) * factor_rotate;
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) * factor_rotate;
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) * factor_rotate;
}
}
}
// compute new T,P
t_current = temperature->compute_scalar();
if (press_couple == 0) {
double tmp = pressure->compute_scalar();
} else {
temperature->compute_vector();
pressure->compute_vector();
}
couple();
// trigger virial computation on next timestep
pressure->addstep(update->ntimestep+1);
// update eta_dot
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
eta_dot += f_eta*dthalf;
eta_dot *= drag_factor;
// update omega_dot
// for non-varying dims, p_freq is 0.0, so omega_dot doesn't change
double f_omega,volume;
if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd;
else volume = domain->xprd*domain->yprd;
double denskt = atom->natoms*boltz*t_target / volume * nktv2p;
for (i = 0; i < 3; i++) {
f_omega = p_freq[i]*p_freq[i] * (p_current[i]-p_target[i])/denskt;
omega_dot[i] += f_omega*dthalf;
omega_dot[i] *= drag_factor;
}
}

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